The circadian clock plays a vital role in the health and fitness of organisms by regulating cellular activities to specific times of the day and night. The long-term goal of this proposal is to understand how circadian clocks function within eukaryotic cells. Forward genetic approaches have been instrumental to initially identify many molecular components of the circadian clock in plants and animals revealing a shared molecular architecture. Recent progress in the circadian field has been focused on the characterization of the precise molecular wiring that builds the clock circuitry which ultimately will uncover how the circadian clocks control daily rhythms in physiology, metabolism and behavior in different species. By developing a complete transcription factor (TF) collection for the model organism Arabidopsis thaliana we have recently implemented a reverse genomic strategy that allowed us refine the transcriptional circuits that build the circadian clock in plants. Based on our initial discoveries we will continue using our TF collection to determine direct regulators of clock genes and implement the discovery of new transcriptional mechanisms by TF-focused gain-of-function screens. In addition, we propose computational approaches to build a map that connects identified clock components with clock-output genes and the genome-wide identification of mechanisms for the non-transcriptional circadian regulation of mRNA and protein levels. In sum, we propose a suite of genomic approaches to expand our transcriptional discovery program and extend our discovery pipeline to the post-transcriptional and post-translational levels. Given the ubiquity and relevance of the circadian clock, the identification of common clock mechanisms will help us understand how alterations in the circadian pacemaker have such a tremendous impact on human well- being.

Public Health Relevance

Almost all organisms possess circadian clocks that control daily rhythms in physiology, metabolism and behavior. The molecular architecture of these clocks appears similar amongst all organisms. Thus the advances learned in model systems such as Arabidopsis will be broadly applicable to understanding rhythms in humans and the known pathologies associated with their dysfunction in a wide range of diseases to impact the treatment of human circadian disorders such as diabetes, SAD, insomnia and jet- lag.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM056006-18
Application #
8651921
Study Section
Cellular Signaling and Regulatory Systems Study Section (CSRS)
Program Officer
Sesma, Michael A
Project Start
1996-09-01
Project End
2017-03-31
Budget Start
2014-04-01
Budget End
2015-03-31
Support Year
18
Fiscal Year
2014
Total Cost
$364,135
Indirect Cost
$85,832
Name
University of Southern California
Department
Biology
Type
Schools of Arts and Sciences
DUNS #
072933393
City
Los Angeles
State
CA
Country
United States
Zip Code
90089
Kang, S Earl; Breton, Ghislain; Pruneda-Paz, Jose L (2018) Construction of Arabidopsis Transcription Factor ORFeome Collections and Identification of Protein-DNA Interactions by High-Throughput Yeast One-Hybrid Screens. Methods Mol Biol 1794:151-182
Li, Zheng; Bonaldi, Katia; Uribe, Francisco et al. (2018) A Localized Pseudomonas syringae Infection Triggers Systemic Clock Responses in Arabidopsis. Curr Biol 28:630-639.e4
Lee, Chin-Mei; Feke, Ann; Li, Man-Wah et al. (2018) Decoys Untangle Complicated Redundancy and Reveal Targets of Circadian Clock F-Box Proteins. Plant Physiol 177:1170-1186
Kubota, Akane; Ito, Shogo; Shim, Jae Sung et al. (2017) TCP4-dependent induction of CONSTANS transcription requires GIGANTEA in photoperiodic flowering in Arabidopsis. PLoS Genet 13:e1006856
Tripathi, Prateek; Carvallo, Marcela; Hamilton, Elizabeth E et al. (2017) Arabidopsis B-BOX32 interacts with CONSTANS-LIKE3 to regulate flowering. Proc Natl Acad Sci U S A 114:172-177
Tripathi, Prateek; Pruneda-Paz, José L; Kay, Steve A (2017) A Modified Yeast-one Hybrid System for Heteromeric Protein Complex-DNA Interaction Studies. J Vis Exp :
Shani, Eilon; Salehin, Mohammad; Zhang, Yuqin et al. (2017) Plant Stress Tolerance Requires Auxin-Sensitive Aux/IAA Transcriptional Repressors. Curr Biol 27:437-444
Huang, He; Alvarez, Sophie; Bindbeutel, Rebecca et al. (2016) Identification of Evening Complex Associated Proteins in Arabidopsis by Affinity Purification and Mass Spectrometry. Mol Cell Proteomics 15:201-17
Breton, Ghislain; Kay, Steve A; Pruneda-Paz, José L (2016) Identification of Arabidopsis Transcriptional Regulators by Yeast One-Hybrid Screens Using a Transcription Factor ORFeome. Methods Mol Biol 1398:107-18
Taylor-Teeples, M; Lin, L; de Lucas, M et al. (2015) An Arabidopsis gene regulatory network for secondary cell wall synthesis. Nature 517:571-5

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